Multiple sequence alignment - TraesCS5D01G053900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G053900 chr5D 100.000 3816 0 0 1 3816 51589993 51586178 0 7047
1 TraesCS5D01G053900 chr5D 96.887 3823 110 6 1 3816 437732625 437728805 0 6392
2 TraesCS5D01G053900 chr5D 94.962 3831 142 34 1 3816 92289731 92293525 0 5958
3 TraesCS5D01G053900 chr2D 96.183 3825 132 13 1 3816 165659792 165663611 0 6242
4 TraesCS5D01G053900 chr2D 94.888 3423 141 20 195 3605 104550644 104547244 0 5321
5 TraesCS5D01G053900 chr1D 94.769 3823 161 27 1 3816 152472507 152476297 0 5915
6 TraesCS5D01G053900 chr1D 96.138 2848 103 6 976 3816 152622850 152625697 0 4643
7 TraesCS5D01G053900 chr7B 94.481 3642 179 18 188 3816 574617111 574620743 0 5592
8 TraesCS5D01G053900 chr7B 94.417 1415 63 11 188 1594 72263846 72265252 0 2161
9 TraesCS5D01G053900 chr7D 96.864 2997 84 8 828 3816 592034288 592037282 0 5005
10 TraesCS5D01G053900 chr7D 94.848 1980 85 12 1 1975 107244658 107242691 0 3075
11 TraesCS5D01G053900 chr7D 96.877 1665 45 5 2158 3816 509207834 509206171 0 2780
12 TraesCS5D01G053900 chr5B 94.891 2427 107 14 195 2610 31741144 31738724 0 3779


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G053900 chr5D 51586178 51589993 3815 True 7047 7047 100.000 1 3816 1 chr5D.!!$R1 3815
1 TraesCS5D01G053900 chr5D 437728805 437732625 3820 True 6392 6392 96.887 1 3816 1 chr5D.!!$R2 3815
2 TraesCS5D01G053900 chr5D 92289731 92293525 3794 False 5958 5958 94.962 1 3816 1 chr5D.!!$F1 3815
3 TraesCS5D01G053900 chr2D 165659792 165663611 3819 False 6242 6242 96.183 1 3816 1 chr2D.!!$F1 3815
4 TraesCS5D01G053900 chr2D 104547244 104550644 3400 True 5321 5321 94.888 195 3605 1 chr2D.!!$R1 3410
5 TraesCS5D01G053900 chr1D 152472507 152476297 3790 False 5915 5915 94.769 1 3816 1 chr1D.!!$F1 3815
6 TraesCS5D01G053900 chr1D 152622850 152625697 2847 False 4643 4643 96.138 976 3816 1 chr1D.!!$F2 2840
7 TraesCS5D01G053900 chr7B 574617111 574620743 3632 False 5592 5592 94.481 188 3816 1 chr7B.!!$F2 3628
8 TraesCS5D01G053900 chr7B 72263846 72265252 1406 False 2161 2161 94.417 188 1594 1 chr7B.!!$F1 1406
9 TraesCS5D01G053900 chr7D 592034288 592037282 2994 False 5005 5005 96.864 828 3816 1 chr7D.!!$F1 2988
10 TraesCS5D01G053900 chr7D 107242691 107244658 1967 True 3075 3075 94.848 1 1975 1 chr7D.!!$R1 1974
11 TraesCS5D01G053900 chr7D 509206171 509207834 1663 True 2780 2780 96.877 2158 3816 1 chr7D.!!$R2 1658
12 TraesCS5D01G053900 chr5B 31738724 31741144 2420 True 3779 3779 94.891 195 2610 1 chr5B.!!$R1 2415

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
935 962 0.251832 TCTTCTTCCTCCTCCGCTGT 60.252 55.000 0.00 0.0 0.00 4.40 F
1289 1319 0.032403 CGTGGTTCGTAGGTGTTCCA 59.968 55.000 0.00 0.0 33.66 3.53 F
1664 1696 1.078708 GGGCAAAGCTAGCGGTACA 60.079 57.895 9.55 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2678 2720 1.113517 ATACCATAGCACCGACCGCT 61.114 55.000 0.0 0.0 43.62 5.52 R
2761 2803 3.072944 CAAGAACAGAGCAAGAGGAAGG 58.927 50.000 0.0 0.0 0.00 3.46 R
2874 2917 4.273480 CAGATCAGGTTGTTGAAGACGTTT 59.727 41.667 0.0 0.0 0.00 3.60 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
211 214 7.119709 TCAATTATTGACGAGAGGTGGATAA 57.880 36.000 3.20 0.00 34.08 1.75
351 359 3.304659 CCATTTTCGACACTCCAAAGGTG 60.305 47.826 0.00 0.00 40.19 4.00
477 493 7.826744 TGTGACACCATGCTATTGTTCTTATTA 59.173 33.333 2.45 0.00 0.00 0.98
587 607 7.724305 AATCGTCAAAGTGTGTACTACATTT 57.276 32.000 0.00 0.00 42.24 2.32
614 634 2.181521 GGAACCGTTTGTGGCACGA 61.182 57.895 13.77 8.59 40.20 4.35
782 809 0.395862 TCTCTGTCCCCGATCCAGAC 60.396 60.000 0.00 0.00 32.16 3.51
935 962 0.251832 TCTTCTTCCTCCTCCGCTGT 60.252 55.000 0.00 0.00 0.00 4.40
1289 1319 0.032403 CGTGGTTCGTAGGTGTTCCA 59.968 55.000 0.00 0.00 33.66 3.53
1445 1477 2.379907 AGGAAATGTGTGGGATGAGGTT 59.620 45.455 0.00 0.00 0.00 3.50
1544 1576 6.235664 TCAAAATGTTCCCACTTCCTAGTAC 58.764 40.000 0.00 0.00 31.96 2.73
1664 1696 1.078708 GGGCAAAGCTAGCGGTACA 60.079 57.895 9.55 0.00 0.00 2.90
1732 1764 7.981789 GGACACATACTGTTCAAGATATTCTCA 59.018 37.037 0.00 0.00 31.03 3.27
1821 1853 6.156949 TCTCTTATGGCATAGACTTTTCCAGT 59.843 38.462 7.35 0.00 39.07 4.00
1850 1882 1.705873 AGAGACGTCCCTGTTTGAGT 58.294 50.000 13.01 0.00 0.00 3.41
1864 1896 7.333423 TCCCTGTTTGAGTTGAAGTTTATATCG 59.667 37.037 0.00 0.00 0.00 2.92
1920 1952 4.551671 AGACAGGCAGGATTAGTCTATGT 58.448 43.478 0.00 0.00 37.75 2.29
1991 2023 2.687370 TGACTAGTCTGTACGCGTACA 58.313 47.619 40.27 40.27 43.14 2.90
2017 2050 1.879380 CTGATCTGGTTGGCGTTGAAA 59.121 47.619 0.00 0.00 0.00 2.69
2440 2482 3.440173 GGTTTATGCAGCAGCTGTTCTTA 59.560 43.478 23.60 7.74 42.74 2.10
2448 2490 4.096984 GCAGCAGCTGTTCTTATACCAATT 59.903 41.667 23.60 0.00 37.91 2.32
2467 2509 3.773860 TTTGTTGCTCGATTGTGTTGT 57.226 38.095 0.00 0.00 0.00 3.32
2676 2718 1.743252 GCAGCCTTCAAGACCTCGG 60.743 63.158 0.00 0.00 0.00 4.63
2678 2720 2.217038 AGCCTTCAAGACCTCGGCA 61.217 57.895 0.00 0.00 43.07 5.69
2737 2779 1.648467 GACCTCTACGTACGGCGGTT 61.648 60.000 21.06 0.00 46.52 4.44
2856 2899 1.519234 GCAGATCGACGCCATCACA 60.519 57.895 0.00 0.00 0.00 3.58
2860 2903 1.075542 GATCGACGCCATCACAAACA 58.924 50.000 0.00 0.00 0.00 2.83
2874 2917 5.993106 TCACAAACAACAACATCGTCATA 57.007 34.783 0.00 0.00 0.00 2.15
2919 2962 6.382282 TCTGATATTGTTCTGAGATCCAGTGT 59.618 38.462 9.98 0.00 43.38 3.55
2997 3042 7.459795 TCGCTTTCACTATAGATCAGATCAT 57.540 36.000 13.14 6.84 0.00 2.45
3032 3077 7.568199 AAGAAACAAGTGCACAACTAGTATT 57.432 32.000 21.04 0.00 38.56 1.89
3108 3153 7.938140 AGCTTGCATCAGTATTTTTACCTAA 57.062 32.000 0.00 0.00 0.00 2.69
3326 3372 6.197903 AGCATATGTATATCTACCCTGCTGA 58.802 40.000 4.29 0.00 35.89 4.26
3435 3482 3.096092 TGTTGGAGTTTCAGGCTTGTTT 58.904 40.909 0.00 0.00 0.00 2.83
3436 3483 3.513515 TGTTGGAGTTTCAGGCTTGTTTT 59.486 39.130 0.00 0.00 0.00 2.43
3561 3608 5.244402 TCTCTTGTGAAATCAAATGCCATGT 59.756 36.000 0.00 0.00 0.00 3.21
3732 3780 9.224058 CGAGCTAGTTCTGTTTACTCTTAATAC 57.776 37.037 4.99 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 138 0.762418 TCGAGTGCCCAAAAGGAAGA 59.238 50.000 0.00 0.00 38.24 2.87
138 140 2.060050 TTTCGAGTGCCCAAAAGGAA 57.940 45.000 0.00 0.00 38.24 3.36
211 214 3.743521 TGCTTGTGTCTCAATAGCTGTT 58.256 40.909 0.00 0.00 35.35 3.16
587 607 2.099921 CACAAACGGTTCCACCAATCAA 59.900 45.455 0.00 0.00 38.47 2.57
614 634 3.661944 GATGTCTGCCATCTCATCGATT 58.338 45.455 0.00 0.00 45.50 3.34
935 962 1.687368 GGGGAGACGAAACCCTAGCTA 60.687 57.143 13.11 0.00 44.97 3.32
1158 1188 2.420372 CTGTTGGAGAGACGAGATCGAA 59.580 50.000 9.58 0.00 43.02 3.71
1248 1278 3.801638 GCAGAAGAAGAGTCAGCTCACAA 60.802 47.826 0.00 0.00 44.00 3.33
1289 1319 1.081892 GTCAACTCGTGCATGCATCT 58.918 50.000 25.64 3.51 0.00 2.90
1337 1368 0.678048 GCCACTGAAGAAATCCGCCT 60.678 55.000 0.00 0.00 0.00 5.52
1664 1696 0.834612 TGGTTTCTCTGGTGTTCCGT 59.165 50.000 0.00 0.00 36.30 4.69
1732 1764 7.559170 AGAATTTCATAGCTAACCTCTGCAATT 59.441 33.333 0.00 0.00 30.37 2.32
1786 1818 4.944619 TGCCATAAGAGATGACGAGAAT 57.055 40.909 0.00 0.00 0.00 2.40
1821 1853 4.529377 ACAGGGACGTCTCTTTGGTATAAA 59.471 41.667 17.30 0.00 0.00 1.40
1850 1882 9.976511 ATCGTCCTATTTCGATATAAACTTCAA 57.023 29.630 0.00 0.00 43.45 2.69
1864 1896 6.276847 AGTGACATCTCAATCGTCCTATTTC 58.723 40.000 0.00 0.00 0.00 2.17
1991 2023 3.031736 ACGCCAACCAGATCAGTAGTAT 58.968 45.455 0.00 0.00 0.00 2.12
2017 2050 6.937436 AAAACGTTGGTCTTCTAAGTTGAT 57.063 33.333 0.00 0.00 0.00 2.57
2167 2204 9.651913 AACAAATTCACATCACTGTTAGTTTTT 57.348 25.926 0.00 0.00 31.62 1.94
2174 2211 6.549364 TCCCTTAACAAATTCACATCACTGTT 59.451 34.615 0.00 0.00 31.62 3.16
2440 2482 5.048083 ACACAATCGAGCAACAAATTGGTAT 60.048 36.000 0.00 0.00 46.45 2.73
2448 2490 2.223456 CCACAACACAATCGAGCAACAA 60.223 45.455 0.00 0.00 0.00 2.83
2467 2509 8.659527 AGTGTACACCAATATCATATGAATCCA 58.340 33.333 22.28 0.00 0.00 3.41
2676 2718 3.264897 CATAGCACCGACCGCTGC 61.265 66.667 1.81 1.81 40.73 5.25
2678 2720 1.113517 ATACCATAGCACCGACCGCT 61.114 55.000 0.00 0.00 43.62 5.52
2761 2803 3.072944 CAAGAACAGAGCAAGAGGAAGG 58.927 50.000 0.00 0.00 0.00 3.46
2851 2894 4.891627 TGACGATGTTGTTGTTTGTGAT 57.108 36.364 0.00 0.00 0.00 3.06
2874 2917 4.273480 CAGATCAGGTTGTTGAAGACGTTT 59.727 41.667 0.00 0.00 0.00 3.60
2997 3042 4.728534 CACTTGTTTCTTTCGTTCACCAA 58.271 39.130 0.00 0.00 0.00 3.67
3032 3077 5.830991 ACACAAGAAAAATACAAGCCCACTA 59.169 36.000 0.00 0.00 0.00 2.74
3120 3166 6.931281 GCACCTGCTAGATGTATTTCAGAATA 59.069 38.462 0.00 0.00 38.21 1.75
3189 3235 5.007682 TCATCCAAGTACTTGCCCTTTTAC 58.992 41.667 27.05 0.00 39.16 2.01
3311 3357 6.995091 GTGAAAATTCTCAGCAGGGTAGATAT 59.005 38.462 0.00 0.00 0.00 1.63
3435 3482 8.048534 AGTACACTTGAAGCTACGAACTATAA 57.951 34.615 0.00 0.00 0.00 0.98
3436 3483 7.551974 AGAGTACACTTGAAGCTACGAACTATA 59.448 37.037 0.00 0.00 0.00 1.31
3561 3608 6.380846 AGCAAGTTGATAAAATAATGCCCAGA 59.619 34.615 7.16 0.00 33.19 3.86
3571 3618 6.863126 GCAAGTGTACAGCAAGTTGATAAAAT 59.137 34.615 7.16 0.00 0.00 1.82
3665 3713 6.974932 AAGAGTATCATGTGTGAATGTGAC 57.025 37.500 0.00 0.00 38.01 3.67


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.